Formula One will never be the same again following the news that Bernie Ecclestone has lost absolute power over the sport he transformed into a global empire.

He will step down as a director of F1's holding company, Delta Topco Limited, after the announcement that he will face criminal proceedings in Germany in April.

Ecclestone will stay in "day-to-day control" of the sport but he will now be answerable to the board's chairman, Peter Brabeck-Letmathe, and his deputy, Donald Mackenzie, ending almost four decades of ultimate control of the most watched global sport, outside football's World Cup and the Olympic Games.

Even if Ecclestone, who has denied any wrongdoing, is cleared of the bribery charges he faces, it is unlikely he will ever again enjoy the unfettered control of the $1bn (£612m) business currently gearing up for the new season, which starts in Melbourne on 16 March.

Although he insisted on Thursday night that it was "complete nonsense" to suggest he will relinquish his control – "The minute the court case is over then I'll be back on the board again," he said – once a dictator's grip on power is loosened it is rarely recovered. Ecclestone's authority was absolute, built up by longevity, myth-making and most of all an unrivalled talent for cutting deals. Now his powers have been neutered, he can never be the same again, and nor can the sport.

Formula One moved swiftly once a Munich court announced that Ecclestone would face charges relating to a $44m payment made to the former German banker Gerhard Gribkowsky. Ecclestone does not deny making the payment but claims he was being blackmailed by Gribkowsky over his tax affairs. But this is only one of the dark clouds circling above the sport's commercial rights holder, who will be 84 this year.

Next month he is likely to hear the verdict of the $141m damages claim from the German media company Constantin Medien over the sale of the sport. And then he faces another action in the United States, where the private equity firm Bluewaters Communications Holdings has filed a lawsuit claiming it should have been sold a stake in F1.

Formula One, for all its superficial success and wealth, is badly run and poorly promoted. It is a sport in urgent need of an overhaul but it was not meant to happen this way. The teams are cash-strapped, apart from the three or four biggest names. Even a marque as big as Lotus, who were fourth last season, did not have enough money to pay their star driver, Kimi Raikkonen.

The teams complain that the owners, CVC Capital Partners, keep too much of the profits and do not invest in the sport. And costs have soared as F1 prepares for a season that will feature the biggest technological changes since 2009, one in which the 2.4 litre V8 engines will be replaced by 1.6 litre turbocharged V6s. Pre-season testing gets under way in Spain in just over a week.

There are too many races (there will be 19 this year) and too many of them are poorly attended, something that does not appear to bother the bosses in the headlong rush to grasp the TV money.

But while the teams complain about Ecclestone – only privately, because they are scared of his vast powers – they are also worried about the future of F1 without the gnomish ringmaster, the son of a Suffolk trawlerman who has been one of the most astute businessmen in all sport. He will limp on for now, badly wounded but not quite toppled. But this truly is the end of an era.

Whoever takes control of Formula One will need to be a big man to shape the sport in the post‑Ecclestone years.